tbuckley/cabot-search huggingface dataset:
Abstract 9: Histological characterization of two genetically engineered mouse models of non-small cell lung cancer
Authors: Nicole F. Leon, David Baliu-Rodriguez, Deepa K. Murugesh, Aimy Sebastian, Gabriela G. Loots, Nicholas R. Hum
Journal: Cancer Research (2023)

Abstract Non-small cell lung cancer (NSCLC) patients exhibit minimal symptoms until late-stage disease, resulting in approximately 80% of patients being diagnosed at advanced stages when the response to therapy is low. Effective pre-clinical models are needed to accurately reflect NSCLC disease progression and improve basic NSCLC research. This work characterizes two genetically engineered mouse models (GEMM) that reflect human NSCLC. These mouse lines utilize a cre recombinase system to induce the expression of two oncogenic mutations (KrasG12D, Trp53fl) in club cells or alveolar epithelial cells based on cell type-specific promoters (Scgb1a1, Sftpc), thereby inducing NSCLC in mice. Furthermore, these mice harbor tumor cell-specific transgenes (GFP, MetRS) for cancer tracking. The MetRS transgene allows tumor cells to incorporate azide-bearing methionine analogs (ANL) into newly synthesized proteins which can then be detected via fluorescent noncanonical amino acid tagging (FUNCAT). Cancer mutations were induced at 6 weeks of age and lung samples were collected for histological analysis at early, mid, and late time points. Histological analysis of the club cell model revealed that hyperplasias are most abundant at the early time point and develop into invasive carcinomas within the bronchioles and alveoli at later time points. Histological scoring of this model showed that tumor burden increased from 28% to 61% of the total lung area after 15 weeks. The alveolar cell model progressed rapidly and exhibited adenocarcinomas and squamous cell carcinomas throughout disease progression. Histological scoring of this model revealed that tumor burden rapidly increased from 55% to 89% of total lung area after 5 weeks. FUNCAT analysis demonstrated that the incorporation of ANL within tumor-bearing mice was cancer-cell-specific. These findings suggest that the GEMM models accurately represent human NSCLC based on their cellular profile, morphology, and localization within the lung. The results also confirm that the tumor cells, and not the normal cells/tissues, are able to incorporate ANL into their proteins via the MetRS transgene. These models have the potential to identify biomarkers of NSCLC progression to improve patient prognosis. *This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-ABS-839507. Citation Format: Nicole F. Leon, David Baliu-Rodriguez, Deepa K. Murugesh, Aimy Sebastian, Gabriela G. Loots, Nicholas R. Hum. Histological characterization of two genetically engineered mouse models of non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 9.
Abstract 2386: Label free imaging for rapid assessment of tumor viability in live tumor fragments
Authors: Jonathan Ouellette, Ellen Wargowski, Eric Wait, Chris Zahm, Scott Johnson, Jon Oliner
Journal: Cancer Research (2023)

Abstract Live tumor fragments (LTF) that maintain a patient's relevant tumor microenvironment provides an opportunity to study treatment response. To verify viability of the fragments over time, we have devised and applied a label-free quantitative microscopy-based approach to monitor LTF health. This method directly assesses intrinsic fluorescence from metabolic co-factors and allows the spatial and temporal visualization of cell status. Using the label-free method of multiphoton fluorescence lifetime microscopy (MP-FLIM), we can assess excised tumor samples over 48 hours to determine the health of individual cells. Specifically, with MP-FLIM, we can analyze signals generated by the intrinsically fluorescent metabolic co-factor NAD(P)H which correlates with mitochondrial outer membrane permeabilization and the irreversible cascades leading to cell death. Our findings using MP-FLIM were confirmed using a standard caspase 3/7 live apoptosis assay. These data demonstrate MP-FLIM can detect and quantify cell viability without the use of potentially toxic dyes, thus enabling longitudinal multi-day studies assessing the effects of therapeutic agents on LTF. Citation Format: Jonathan Ouellette, Ellen Wargowski, Eric Wait, Chris Zahm, Scott Johnson, Jon Oliner. Label free imaging for rapid assessment of tumor viability in live tumor fragments [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2386.
Abstract 1494: PBRM1-deficient PBAF complexes target de novo genomic loci to activate NF-κB pathway in clear cell renal cell carcinoma
Authors: Xiaosai Yao, Jing Han Hong, Amrita Nargund, Michelle Shu Wen Ng, Hong Lee Heng, Zhimei Li, Peiyong Guan, Masahiro Sugiura, Pek Lim Chu, Loo Chien Wang, Xiaofen Ye, Robert Yauch, Kenneth Tou-En Chang, Radoslaw M. Sobota, Patrick Tan, Bin Tean Teh
Journal: Cancer Research (2023)

Abstract PBRM1 is an accessory subunit of the PBAF subclass of the SWI/SNF chromatin remodeler and the inactivation of PBRM1 is the second most frequent mutational event in kidney tumorigenesis. However, the impact of PBRM1 loss on chromatin remodeling, especially pertaining to kidney tumorigenesis, has not been examined previously. Here we show that in VHL-deficient ccRCC tumors, PBRM1 deficiency results in altered PBAF complexes that retain the association between SMARCA4 and ARID2 but disengage BRD7 from SMARCA4. The PBRM1-deficient PBAF complexes redistribute from promoter proximal regions to distal enhancer regions containing motifs of pro-tumorigenic factors including NF-κB. Subsequently, PBRM1-deficient cells display heightened NF-κB activity across multiple cell models. The ATPase function of SMARCA4 maintains chromatin occupancy of both pre-existing and newly acquired RELA specific to PBRM1 loss, and activates downstream target gene expression. Proteasome inhibitor bortezomib reverses NF-κB activation by reducing RELA occupancy and delays growth of PBRM1-deficient tumors. In conclusion, PBRM1 safeguards the chromatin by repressing aberrant liberation of pro-tumorigenic NF-κB target genes by residual PBRM1-deficient PBAF complexes. Citation Format: Xiaosai Yao, Jing Han Hong, Amrita Nargund, Michelle Shu Wen Ng, Hong Lee Heng, Zhimei Li, Peiyong Guan, Masahiro Sugiura, Pek Lim Chu, Loo Chien Wang, Xiaofen Ye, Robert Yauch, Kenneth Tou-En Chang, Radoslaw M. Sobota, Patrick Tan, Bin Tean Teh. PBRM1-deficient PBAF complexes target de novo genomic loci to activate NF-κB pathway in clear cell renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1494.
Abstract 605: Single cell RNA sequencing reveals tumor immune microenvironment and T cell receptor diversity in epidermal growth factor receptor <i>(EGFR)</i> mutated lung cancer
Authors: Turja Chakrabarti, Wei Wu, Daniel L. Kerr, Paul Allegakoen, Trever G. Bivona, Collin M. Blakely
Journal: Cancer Research (2023)

Abstract Background: Somatic alterations in the Epidermal Growth Factor Receptor (EGFR) gene represent a common subset of oncogene-driven lung cancer. Patients who receive EGFR-targeted tyrosine kinase inhibitor (TKI) therapy inevitably develop treatment resistance with limited options after disease progression, with immune checkpoint inhibitor therapy (ICI) typically ineffective. Tumor Immune Microenvironment (TME) characteristics, including T-cell receptor (TCR) sequencing and clonality have been incompletely explored in this population. Methods: We further analyzed our group’s available data from a previous study on therapy-induced evolution of human lung cancer (Maynard et. al, PMID: 32822576). Tumor samples were sorted and subjected to smartseq-based single-cell RNA sequencing. A total of 7495 cells were derived from 17 samples from 10 patients with tumors that harbored EGFR driver gene mutations. This included 1322 gene marker-annotated T-cells. Samples were grouped into three treatment conditions: treatment naïve (TN), residual disease (RD), and progressive disease (PD). We then used the TraCeR tool to infer the TCR α, β, and the complementarity-determining region 3 (CDR3) sequences. Results: T-cells were enriched in RD (55.2%) relative to TN (12.8%) and PD (31.9%) (p&amp;lt;0.0001, Chi-square test) with cytotoxic T-cells as the predominant phenotype across treatment conditions. Increased expression of CTLA4, and LAG3 occurred in PD (p&amp;lt;0.0001, Kruskal-Wallis test). Single-cell TCR analysis revealed increased TCR clonal diversity in PD (Shannon Diversity Index: 0.261 PD &amp;gt; 0.255 TN &amp;gt; 0.205 RD) while increased clonal expansion occurred in RD (32 clones from 4 patients) as compared to TN (17 clones from 1 patient) and PD (14 clones from 1 patient) (p&amp;lt;0.0001, Chi-square test). Conclusion: T-cell infiltration is greatest in RD, while immunosuppressive genes were significantly expressed in PD. Increased TCR clonal expansion with less clonal diversity in RD suggests the presence of tumor-specific TCR clones and that this may be the optimal time to initiate ICI treatment. Future directions will include the identification of clonally expanded TCR and matched neoantigens to provide potential tailored immunotherapies for patients with TKI-resistant tumors. Citation Format: Turja Chakrabarti, Wei Wu, Daniel L. Kerr, Paul Allegakoen, Trever G. Bivona, Collin M. Blakely. Single cell RNA sequencing reveals tumor immune microenvironment and T cell receptor diversity in epidermal growth factor receptor (EGFR) mutated lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 605.
Abstract 746: Disparities in factors affecting access to palliative care in patients with stage IV breast cancer
Authors: Mira Itani, Saad Sabbagh, Mohamed Mohanna, Barbara Dominguez, Hong Liang, Zeina Nahleh
Journal: Cancer Research (2023)

Abstract Background: Palliative care is an essential component of cancer care; however, factors hindering its reach to the target population remain understudied. We aim to explore whether an association exists between socioeconomic and geographic factors and access to palliative care (PC) in patients with Stage IV breast cancer in the US. Methods: This 2004-2017 National Cancer Database analysis includes patients with Stage IV breast cancer who received palliative care. Access to PC is defined as being either at the patient’s primary healthcare facility or at a referral site. Chi-square tests and a multivariate logistic regression were performed to determine the independent factors predicting access to PC. SAS version 9.4 was used to analyze the data. Results: A total of 18,903 patients were included in the analysis: 15,111 received palliative care services at the same facility and 3,792 were referred elsewhere. Patient age, race, insurance status, Charlson-Deyo score, setting, high school diploma status, median income, facility type, facility location, and distance from healthcare centers were all significantly different between the two groups. On logistic regression, better odds for access to PC were predicted by urban settings (OR: 1.47; 95% CI: 1.30 - 1.67) and being in the Middle Atlantic region (OR: 1.27; 95% CI: 1.07 - 1.52). Distance from the healthcare facility of 4 miles or greater predicted worse odds for access to PC. Comprehensive cancer programs (OR: 1.60; 95% CI: 1.43 - 1.80) and academic/research programs (OR: 2.40; 95% CI: 2.11 - 2.73) held higher odds for access to PC. Having Medicaid/other government insurance (OR: 1.43; 95% CI: 1.24 - 1.65) predicted better odds for access to PC. However, having no insurance was also found to increase access to PC (OR: 1.30; 95% CI: 1.08 - 1.55). Median income and high school diploma status were not significantly associated with the outcome. Conclusion: PC was positively affected by having access to urban settings, nearby healthcare centers, non-community care centers, Medicaid/other governmental insurance, and by being in the Middle Atlantic region of the US. Having no insurance appears to increase palliative care use, which was unexpected but could be explained if patients with no insurance did not receive standard treatment and were instead offered palliative care. This needs to be investigated in future research. Citation Format: Mira Itani, Saad Sabbagh, Mohamed Mohanna, Barbara Dominguez, Hong Liang, Zeina Nahleh. Disparities in factors affecting access to palliative care in patients with stage IV breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 746.
Abstract 3743: circPMS1 is a pro-metastatic circular RNA in melanoma
Authors: Nicol Mecozzi, Olga Vera, Florian Karreth
Journal: Cancer Research (2023)

Abstract Deregulated gene expression is a major driver of melanoma metastasis, a process that results in the majority of melanoma-related deaths. Importantly, these alterations are not limited to protein-coding mRNAs, but also include noncoding RNAs. Despite many recent studies implicating circular RNAs (circRNAs) in cancer development, it is unknown if their deregulation contributes to melanoma metastasis. To identify circRNAs with putative roles in melanomagenesis, we performed RNA sequencing on a panel of melanoma and melanocyte cell lines. 21 differentially expressed circRNAs were validated by qPCR and Sanger sequencing of the backsplice junction. Further analyses of the ratio of the circular and cognate linear RNA transcripts and expression in a larger panel of cell lines identified circPMS1 as a circRNA that is upregulated in melanoma through enhanced backsplicing of the linear PMS1 mRNA. Using transposon-mediated delivery, we examined the effects of stable circPMS1 overexpression on melanoma cells. While proliferation and focus formation were not impacted, migration and invasion were enhanced by circPMS1. Moreover, tail vein injection of circPMS1 overexpressing melanoma cells increased lung metastasis. In addition to this transplant model, we generated the first genetically engineered mouse model of melanoma overexpressing a pro-tumorigenic circRNA. These mice are currently being analyzed. Mechanistically, we find that circularization is required for the pro-migratory effects of the circPMS1 overexpression construct. Additionally, circPMS1 harbors the canonical PMS1 start codon, a predicted ORF spanning over the backsplice junction, and a predicted IRES sequence. Indeed, inserting a flag-tag in the overexpression construct revealed circPMS1 to be translated into a truncated 25kD PMS1 protein as well as a 20kD protein likely arising from an in-frame downstream start codon. Importantly, these truncated circPMS1 proteins are endogenously expressed and increased in melanoma compared to melanocytes while the full-length PMS1 protein is evenly expressed. These findings suggest that circPMS1 promotes melanoma metastasis, at least in part, by coding for truncated circPMS1 proteins. Further work will establish the functions of the circPMS1-encoded proteins and their roles in driving melanoma progression and metastasis. Citation Format: Nicol Mecozzi, Olga Vera, Florian Karreth. circPMS1 is a pro-metastatic circular RNA in melanoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3743.
Abstract 3665: Umbilical cord blood endothelial progenitor cell-derived extracellular vesicles control important endothelial cell functions
Authors: Sawssen Ben Fraj, Sina Naserian, Bileyle Lorenzini, Sylvie Goulinet, Philippe Mauduit, Georges Uzan, Houda Haouas
Journal: Cancer Research (2023)

Abstract Background: Circulating endothelial progenitor cells (EPCs) play a pivotal role in vascular regeneration and the repair of diseases in which angiogenesis is required, including ischemia and tissue transplantation. Although they are a potentially valuable cell therapy tool, their clinical use remains limited due to suboptimal storage conditions and especially, immune rejection. Even if these cells have been shown to be tolerated by the immune system, their in vivo long-term effects still remain to be elucidated. EPC-derived extracellular vesicles (EPC-EVs) may be an attractive alternative to EPCs given their key role in cell-cell communication and expression of the same parental markers. In this study, we investigated the regenerative effects of umbilical cord blood EPC-EVs on EPCs in vitro. Methods: EPCs were obtained from human umbilical cord blood (CB) and characterized by flow cytometry. After amplification, EPCs were cultured in a medium containing an EVs-depleted serum (EV-free medium). Then the conditioned medium was used to isolate the EVs with Tangential Flow Filtration (TFF). The EVs were characterized by a series of tests defining their size, number, and protein content. The regenerative effects of EPC-EVs on endothelial cells were investigated by analyzing cell migration, wound healing, and tube formation. We also analyzed the effect of EPC-EVs on endothelial cell inflammation and NO production. Results: We showed that adding different doses of EPC-EVs on EPCs does not alter the basal expression of the endothelial cell markers CD31, CD144, and KDR, nor change their proliferative potential and NO production level. Furthermore, we demonstrated that EPC-EVs, when used at a higher than physiologic dose, create a mild inflammatory condition that activates EPCs and boosts their regenerative features like migration and tube formation functions. Conclusions: Our results reveal for the first time that EPC-EVs, when used at a high dose, could enhance EPC regenerative functions without altering their endothelial identity. Citation Format: Sawssen Ben Fraj, Sina Naserian, Bileyle Lorenzini, Sylvie Goulinet, Philippe Mauduit, Georges Uzan, Houda Haouas. Umbilical cord blood endothelial progenitor cell-derived extracellular vesicles control important endothelial cell functions. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3665.
Abstract 3990: Imaging molecular alterations during tucatinib response in preclinical models of HER2+ breast cancer
Authors: Patrick Song, Ameer Mansur, Anna Sorace
Journal: Cancer Research (2023)

Abstract Introduction: Human epidermal growth factor receptor 2 (HER2) is overexpressed in 25% of breast cancers. Tucatinib, a small molecule HER2 inhibitor, was FDA approved for inoperable or metastatic HER2+ breast cancer. As many of these patients have inoperable tumors, there is a need to identify imaging metrics that can characterize response to tucatinib. Positron emission tomography (PET) imaging can quantify changes in the tumor microenvironment that precede changes in tumor size through imaging with radiopharmaceuticals that target proliferation (fluorothymidine, [18F]-FLT), hypoxia (fluoromisonidazole, [18F]-FMISO) and HER2 expression ([89Zr]-Pertuzumab). The goal of this study is to use advanced PET imaging to non-invasively monitor response to tucatinib in HER2+ primary breast cancer and quantify the subsequent tumor microenvironment modulation. Methods: HER2+ cell line (BT474) and patient derived xenograft (BCM 3472) tumor models were engrafted and developed to 270 ± 166.4 mm3 before being enrolled into experiments. Mice were treated with 50 mg/kg tucatinib via PO and were imaged with [18F]-FLT PET (N = 8) on days 0, 3 and 7, [18F]-FMISO PET (N = 6) on days 0, 3 and 7, or [89Zr]-Pertuzumab PET (N = 5) on days 0 and 14. Intratumoral proliferation, hypoxia and HER2 expression were quantified with standardized uptake value (SUV). Following the final imaging timepoint, tumors were excised for immunohistochemistry against Ki-67 (proliferation), pimonidazole (hypoxia), and HER2. A non-parametric T-test was used to assess for significance. Results: Tucatinib treated BT474 and BCM3472 tumors had a 2.07 and 2.63 fold decrease in tumor volume, respectively (p&amp;lt;0.01). Tucatinib treated BT474 and BCM3472 tumors had significantly decreased hypoxia and proliferation, relative to control tumors (p&amp;lt;0.05). Tucatinib treated BT474 tumors had significantly decreased HER2 expression (p&amp;lt;0.05); however, no significant change in HER2 expression was observed in tucatinib treated BCM3472 tumors. Conclusion: Tucatinib significantly decreases tumor volume and decreases intratumoral proliferation and hypoxia in both cell-line and patient-derived xenograft models of HER2+ breast cancer. Our data suggests molecular imaging may drive understanding of and predict response to tucatinib therapy. Acknowledgements: Tucatinib was provided by Seagen Inc. Bothell, Washington, USA. Citation Format: Patrick Song, Ameer Mansur, Anna Sorace. Imaging molecular alterations during tucatinib response in preclinical models of HER2+ breast cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3990.